[Chimera-users] adding an O in compound 1

Eric Pettersen pett at cgl.ucsf.edu
Tue Jun 18 11:13:01 PDT 2013

As Elaine says, the Mol2 type of the oxygen atoms in an oxygen molecule is O.2.  In a structure with poor bond lengths, Chimera will sometimes guess that the oxygen molecule is instead a hydrogen peroxide, where the oxygens are O.3.


On Jun 18, 2013, at 9:59 AM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Hi Ibai,
> If you are asking what atom type GOLD will accept, I recommend asking the GOLD developers.  All I can say is that O.3 is one of the commonly used atom types in the mol2 format, as listed here:
> <http://www.tripos.com/mol2/atom_types.html>
> Looking at diagrams of Compound I, I would guess O.2 instead, but that is based purely on chemistry.  I don't know anything about the input requirements of GOLD.
> Best,
> Elaine
> ----------
> Elaine C. Meng, Ph.D. 
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> On Jun 17, 2013, at 10:28 AM, Ibai Gazpio <ibaigazpio at gmail.com> wrote:
>> Hi all,
>> I'm trying to add an O molecule as compound 1 bound to a Fe of an Hem group. I use a program called GOLD to perform dockings but this doesn't recognize this O atom type, that is a O.3 type.. The output should be a mol2 file. Which atom type should I use?
>> Ibai.
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